It is particularly preferred to employ Staphylococcal genes and gene products as targets for the development of antibiotics. The Staphylococci make up a medically important genera of microbes. They are known to produce two types of disease, invasive and toxigenic. Invasive infections are characterized generally by abscess formation effecting both skin surfaces and deep tissues. S. aureus is the second leading cause of bacteremia in cancer patients. Osteomyelitis, septic arthritis, septic thrombophlebiuis and acute bacterial endocarditis are also relatively common. There are at least three clinical conditions resulting from the toxigenic properties of Staphylococci. The manifestation of these diseases result from the actions of exotoxins as opposed to tissue invasion and bacteremia. These conditions include: Staphylococcal food poisoning, scalded skin syndrome and toxic shock syndrome
The frequency of Staphylococcus aureus infections has risen dramatically in the past 20 years. This has been attributed to the emergence of multiply antibiotic resistant strains and an increasing population of people with weakened immune systems. It is no longer uncommon to isolate Staphylococcus aureus strains which are resistant to some or all of the standard antibiotics. This has created a demand for both new anti-microbial agents and diagnostic tests for this organism.
Transcription of DNA is often arrested at sites in DNA that trap a fraction of elongating RNA polymerase molecules that pass through, resulting in blocked ternary complexes that cannot propagate or dissociate their RNA product. Transcript cleavage factors induce RNA polymerase to cleave the RNA in such complexes at the 3'-end, allowing RNA polymerase to back up and re-attempt to read through the potential trap (Borukhov et al. 1993. Cell 72:459-466). In addition to assuring efficient transcript elongation, transcript cleavage factors increase the fidelity of transcription since misincorporated bases at the 3'-end of the nascent RNA also lead to arrested complexes (Erie et al. Science 262:867-8730. Two transcript cleavage factors, GreA and GreB, have been identified in E. coli (Borukhov et al. 1993. Cell 72:459-466). GreA-dependent transcript cleavage usually results in the removal of di- and trinucleotides from the 3'-end of the stalled RNA. GreB-dependent cleavage yields larger oligonucleotides, up to a length of nine nucleotides. Both proteins bind RNA polymerase. Neither the GreA or GreB proteins possess intrinsic nuclease activity rather they stimulate a nuclease activity inherent in RNA polymerase (Orlova et al. 1995. Proc. Natl. Acad. Sci., USA 92:4596-4600). The GreA and GreB proteins are homologous, sharing 38% sequence identity (59% similar). The eukaryotic transcript elongation protein SII is similar to the GreA and GreB proteins in that it stimulates RNA cleavage from the 3'-end of RNA in a stalled complex but does not share significantly sequence homology with the GreA and GreB proteins (Borukhov et al. 1993. Cell 72:459-466).
Clearly, there is a need for factors, such as the novel compounds of the invention, that have a present benefit of being useful to screen compounds for antibiotic activity. Such factors are also useful to determine their role in pathogenesis of infection, disfunction and disease. There is also a need for identification and characterization of such factors and their antagonists and agonists which can play a role in preventing, ameliorating or correcting infections, disfunctions or diseases.
The polypeptides of the invention have amino acid sequence homology to a known E. coli greA protein.